Later (1952–54) he served as Deputy Commander of Operations Department of General Staff, Commander of Planning Department of IDF. In this role, he helped organize the IDF into a reservist-based army, developed the mobilization system, and wrote the first draft of the Israel defense doctrine.

Ne'eman was founder and director of the School of Physics and Astronomy at Tel Aviv University from 1965 to 1972, president of Tel Aviv University from 1971 to 1975, and director of its Sackler Institute of Advanced Studies from 1979 to 1997. He was also the co-director (along with Sudarshan) of the Center for Particle Theory at the University of Texas, Austin from 1968 to 1990. He was a strong believer in the importance of space research and satellites to Israel's economic future and security, and thus founded the Israeli Space Agency in 1983, which he chaired almost until his death. He also served on the Atomic Energy Commission from 1965 to 1984 and held the position of scientific director in its Soreq facility. Neeman was chief scientist of the Defense Ministry from 1974 to 1976.

He was described as "one of the most colorful figures of modern science"[5] and co-authored The Particle Hunters, which was published in English in 1986. The Times Literary Supplement hailed this book as "the best guide to quantum physics at present available".[6]

In 1984, he received the Wigner Medal, which is awarded every 2 years for "outstanding contributions to the understanding of physics through group theory."

In 2003, he received the EMET Prize for Arts, Sciences and Culture for his pioneering contribution in the deciphering of the atomic nucleus and its components, and for his enormous scientific contribution to the development of sub-atomic physics in Israel.

He was also awarded with the College de France Medal and the Officer's Cross of the French Order of Merit (Paris, 1972), the Wigner Medal (Istanbul-Austin, 1982), Birla Science Award (Hyderabad, 1998) and additional prizes and honorary doctorates from universities in Europe and USA.[8]

He retained his seat in the 1984 elections, but Tehiya were not included in the grand coalition formed by the Alignment and Likud. After the 1988 elections, Tehiya were again excluded from the governing coalition. Ne'eman resigned from the Knesset on 31 January 1990 and was replaced by Gershon Shafat. However, Tehiya joined the government in June after the Alignment had left, and he was appointed Minister of Energy and Infrastructure and Minister of Science and Technology despite not retaking his seat in the Knesset. He lost his ministerial position following the 1992 elections and did not return to politics.